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core::scoring::hbonds::NPDHBondSet Class Reference

A class that holds Hbond objects and helps setup Hbonds for scoring. More...

#include <NPDHBondSet.hh>

Inheritance diagram for core::scoring::hbonds::NPDHBondSet:
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Public Member Functions

 NPDHBondSet ()
 
 ~NPDHBondSet () override
 
 NPDHBondSet (Size const nres)
 
 NPDHBondSet (HBondOptions const &options)
 
 NPDHBondSet (HBondOptions const &options, Size const nres)
 
 NPDHBondSet (pose::Pose &pose, EnergyMap const &weights)
 convenience constructor: Find all the hbonds in the pose. BB only default. More...
 
 NPDHBondSet (HBondOptions const &options, pose::Pose &pose, EnergyMap const &wights)
 convenience constructor: Find all the hbonds in the pose. BB only default. More...
 
 NPDHBondSet (NPDHBondSet const &src)
 copy ctor More...
 
 NPDHBondSet (NPDHBondSet const &src, utility::vector1< core::Size > const &exclude_list)
 NOTE: this is going to be wrong... More...
 
 NPDHBondSet (NPDHBondSet const &src, utility::vector1< bool > const &residue_mask)
 
 NPDHBondSet (NPDHBondSet const &src, Size seqpos)
 copy ctor More...
 
void setup_for_residue_pair_energies (pose::Pose const &pose, bool const calculate_derivative=false)
 
basic::datacache::CacheableDataOP clone () const override
 Clone this object. More...
 
void show (std::ostream &out) const
 Print just the information stored in each individual hbond. More...
 
void show () const
 
void show (pose::Pose const &pose, bool const print_header, std::ostream &out) const
 Print nicely formated summary of the hbonds and their geometry in the pose. More...
 
void show (pose::Pose const &pose, bool const print_header=true) const
 
void show (pose::Pose const &pose, Size const residue, bool const print_header, std::ostream &out) const
 Print nicely formated summary of all the hbonds to a specific residue. More...
 
void show (pose::Pose const &pose, Size const residue, bool const print_header=true) const
 
Real hbond_weight (id::AtomID const &id, Size hbond_index) const
 Return the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom – stored in HBond::acc_index() or HBond::don_index()) More...
 
Real d_hbond_weight_dE (id::AtomID const &id, Size hbond_fixed_index, Size hbond_changing_index) const
 Return the derivative of the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom ) as a function of the change in energy of another (possibly the same) hbond (by index) given the AtomID of the acceptor or the donor. More...
 
Real dEtot_dEhb (Size hbond_index) const
 Return the derivative for the system induced by a change in energy of a particular hbond as caused by movement by its atoms. More...
 
- Public Member Functions inherited from core::scoring::hbonds::HBondSet
 HBondSet ()
 
 ~HBondSet () override
 
 HBondSet (Size const nres)
 
 HBondSet (HBondOptions const &options)
 
 HBondSet (HBondOptions const &options, Size const nres)
 
 HBondSet (pose::Pose &pose, bool const bb_only=true)
 Convenience constructor: Find all the hbonds in the pose. BB only default. More...
 
 HBondSet (HBondOptions const &options, pose::Pose &pose, bool const bb_only=true)
 Convenience constructor: Find all the hbonds in the pose. BB only default. More...
 
 HBondSet (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::scoring::hbonds::HBondDatabase const &database)
 Convenience constructor: Find all the hbonds between two residues. BB only default. More...
 
 HBondSet (HBondOptions const &options, core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::scoring::hbonds::HBondDatabase const &database)
 Convenience constructor: Find all the hbonds between two residues. BB only default. More...
 
 HBondSet (HBondSet const &src)
 copy ctor More...
 
 HBondSet (HBondSet const &src, utility::vector1< core::Size > exclude_list)
 copy ctor More...
 
 HBondSet (HBondSet const &src, utility::vector1< bool > residue_mask)
 copy ctor More...
 
 HBondSet (HBondSet const &src, Size seqpos)
 copy ctor More...
 
void setup_for_residue_pair_energies (pose::Pose const &pose, bool const calculate_derivative=false, bool const backbone_only=true)
 
HBond const & hbond (Size const number) const
 Access hbond. More...
 
HBondCOP hbond_cop (Size const number) const
 Access hbond. More...
 
utility::vector1< HBondCOPatom_hbonds (AtomID const &atom, bool include_only_allowed=true) const
 Get a vector of the hbonds involving a particular atom. More...
 
utility::vector1< HBondCOP >
const & 
atom_hbonds_all (AtomID const &atom) const
 Get a reference to a vector of all the hbonds involving a particular atom; in contrast to "atom_hbonds" (above), this function does not exclude sc/bb hydrogen bonds. More...
 
utility::vector1< HBondCOPresidue_hbonds (Size const seqpos, bool include_only_allowed=true) const
 Get a vector of all the hbonds involving this residue. More...
 
Size nhbonds () const
 Number of hbonds. More...
 
utility::vector1< HBondOP > const & hbonds () const
 Return the vector of HBond pointers. More...
 
Size nhbonds (Size const seqpos, bool include_only_allowed=true) const
 Number of hbonds involving this residue. More...
 
Size nhbonds (AtomID const &atom, bool include_only_allowed=true) const
 Number of hbonds involving this atom. More...
 
int nbrs (Size const seqpos) const
 general function for accessing the number of 10A neighbors of a given position set by setup_for_residue_pair_energies. More...
 
HBondOptions const & hbond_options () const
 Read access to the stored hbond options. More...
 
bool allow_hbond (Size const index) const
 Is this hbond allowed under the bb-bb exclusion scheme? More...
 
bool allow_hbond (HBond const &hbond) const
 
bool acc_bbg_in_bb_bb_hbond (Size const residue) const
 is the backbone bone acceptor group in a bb/bb hydrogen bond? More...
 
bool don_bbg_in_bb_bb_hbond (Size const residue) const
 is the backbone bone donor group in a bb/bb hydrogen bond? More...
 
void append_hbond (Size const dhatm, conformation::Residue const &don_rsd, Size const aatm, conformation::Residue const &acc_rsd, HBEvalTuple const &hbe_tuple, Real const energy, Real const weight, HBondDerivs const &deriv)
 Add a new hbond to the list updates the "hbchk" array as necessary. More...
 
void set_hbond_options (HBondOptions const &options)
 set the hbond options for this hbond set; clears all hbonds already stored More...
 
void sort_by_weighted_energy ()
 
void clear ()
 Delete all the data. More...
 
void set_backbone_backbone_acceptor (Size const residue, bool state)
 Manually set the state of backbone-backbone acceptor. Used for symmetry. More...
 
void set_backbone_backbone_donor (Size const residue, bool state)
 Manually set the state of backbone-backbone donor. Used for symmetry. More...
 
void resize_bb_donor_acceptor_arrays (Size const new_dimension)
 Resize bb info arrays. More...
 
void copy_bb_donor_acceptor_arrays (HBondSet const &src)
 
void set_nbrs (Size const seqpos, Size value)
 Used by SymmetricScorFunction. Not sure why. Not for general use. More...
 
basic::datacache::CacheableDataOP clone () const override
 Clone this object. More...
 
void show (std::ostream &out) const
 Print just the information stored in each individual hbond. More...
 
void show () const
 
void show (pose::Pose const &pose, bool const print_header, std::ostream &out) const
 Print nicely formated summary of the hbonds and their geometry in the pose. More...
 
void show (pose::Pose const &pose, bool const print_header=true) const
 
void show (pose::Pose const &pose, Size const residue, bool const print_header, std::ostream &out) const
 Print nicely formated summary of all the hbonds to a specific residue. More...
 
void show (pose::Pose const &pose, Size const residue, bool const print_header=true) const
 

Private Types

typedef id::AtomID AtomID
 
typedef HBondSet parent
 

Private Member Functions

void derive_per_hbond_donor_and_acceptor_weights (pose::Pose const &pose)
 
void get_weights_for_one_partner_hbonder (id::AtomID jj_id)
 
void get_weights_for_two_partner_hbonder (id::AtomID jj_id)
 
void sum_dEtot_dEhb_for_atom (id::AtomID const &jj_id)
 

Private Attributes

EnergyMap sfxn_weights_
 The weights (in particular, for the npd_hbond_* terms) that will be used to determine the donor and acceptor weights. More...
 
id::AtomID_Map
< utility::vector1< Real > > 
atom_hbond_energies_
 One (unweighted) energy per hbond per atom. More...
 
id::AtomID_Map
< utility::vector1< Real > > 
atom_hbond_sfxn_wtd_energies_
 One score-function weighted energy per hbond per atom. More...
 
id::AtomID_Map
< utility::vector1< Real > > 
atom_hbond_weights_
 One weight per hbond per atom. More...
 
id::AtomID_Map
< utility::vector1
< utility::vector1< Real > > > 
dwt_dE_for_hbond_
 d wt / d E so that this needs to be calculated only once per hydrogen bond More...
 
utility::vector1< RealdEtot_dEhb_
 

Friends

std::ostream & operator<< (std::ostream &out, const NPDHBondSet &hbond_set)
 
bool operator== (NPDHBondSet const &a, NPDHBondSet const &b)
 equality operator More...
 

Additional Inherited Members

- Protected Member Functions inherited from core::scoring::hbonds::HBondSet
void hbond_don_npd_weight (Size index, Real setting)
 allow the NPDHBondSet to store the npd weights in the hbond objects More...
 
void hbond_acc_npd_weight (Size index, Real setting)
 allow the NPDHBondSet to store the npd weights in the hbond objects More...
 

Detailed Description

A class that holds Hbond objects and helps setup Hbonds for scoring.

For general hydrogen bond information, either use the default or option constructor, then use the fill methods in hbonds.hh OR use the convenience constructors to detect all Hbonds. Use the copy constructors to fill NPDHBondSets with the Hydrogen bonds you are interested in.

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( )
core::scoring::hbonds::NPDHBondSet::~NPDHBondSet ( )
overridedefault
core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( Size const  nres)
core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( HBondOptions const &  options)
core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( HBondOptions const &  options,
Size const  nres 
)
core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( pose::Pose pose,
EnergyMap const &  weights 
)

convenience constructor: Find all the hbonds in the pose. BB only default.

convenience constructor. If you need more controlled construction please use one of the other constructors

The pose must be non-const because the neighbor graph may need to be initialized.

References derive_per_hbond_donor_and_acceptor_weights().

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( HBondOptions const &  opts,
pose::Pose pose,
EnergyMap const &  weights 
)

convenience constructor: Find all the hbonds in the pose. BB only default.

convenience constructor. If you need more controlled construction please use one of the other constructors

The pose must be non-const because the neighbor graph may need to be initialized.

References derive_per_hbond_donor_and_acceptor_weights().

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( NPDHBondSet const &  src)

copy ctor

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( NPDHBondSet const &  src,
utility::vector1< core::Size > const &  exclude_list 
)

NOTE: this is going to be wrong...

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( NPDHBondSet const &  src,
utility::vector1< bool > const &  residue_mask 
)
core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( NPDHBondSet const &  src,
Size  seqpos 
)

copy ctor

Member Function Documentation

basic::datacache::CacheableDataOP core::scoring::hbonds::NPDHBondSet::clone ( ) const
override

Clone this object.

clone this object

Real core::scoring::hbonds::NPDHBondSet::d_hbond_weight_dE ( id::AtomID const &  id,
Size  hbond_fixed_index,
Size  hbond_changing_index 
) const

Return the derivative of the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom ) as a function of the change in energy of another (possibly the same) hbond (by index) given the AtomID of the acceptor or the donor.

References dwt_dE_for_hbond_.

void core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights ( pose::Pose const &  pose)
private
Real core::scoring::hbonds::NPDHBondSet::dEtot_dEhb ( Size  hbond_index) const

Return the derivative for the system induced by a change in energy of a particular hbond as caused by movement by its atoms.

References dEtot_dEhb_.

void core::scoring::hbonds::NPDHBondSet::get_weights_for_one_partner_hbonder ( id::AtomID  jj_id)
private
void core::scoring::hbonds::NPDHBondSet::get_weights_for_two_partner_hbonder ( id::AtomID  jj_id)
private
Real core::scoring::hbonds::NPDHBondSet::hbond_weight ( id::AtomID const &  id,
Size  hbond_index 
) const

Return the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom – stored in HBond::acc_index() or HBond::don_index())

References atom_hbond_weights_.

void core::scoring::hbonds::NPDHBondSet::setup_for_residue_pair_energies ( pose::Pose const &  pose,
bool const  calculate_derivative = false 
)
void core::scoring::hbonds::NPDHBondSet::show ( std::ostream &  out) const

Print just the information stored in each individual hbond.

References core::scoring::hbonds::HBondSet::hbond(), and core::scoring::hbonds::HBondSet::nhbonds().

Referenced by core::scoring::hbonds::operator<<().

void core::scoring::hbonds::NPDHBondSet::show ( ) const

References core::scoring::hbonds::TR().

Referenced by show().

void core::scoring::hbonds::NPDHBondSet::show ( pose::Pose const &  pose,
bool const  print_header,
std::ostream &  out 
) const

Print nicely formated summary of the hbonds and their geometry in the pose.

Optionally print a header, and then a row for each hydrogen bond in the set using the iterprable version of the hbond show format formatted for easy parsing by R, Excel, etc.

References core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), and core::scoring::hbonds::HBond::show().

void core::scoring::hbonds::NPDHBondSet::show ( pose::Pose const &  pose,
bool const  print_header = true 
) const
void core::scoring::hbonds::NPDHBondSet::show ( pose::Pose const &  pose,
Size const  residue_number,
bool const  print_header,
std::ostream &  out 
) const

Print nicely formated summary of all the hbonds to a specific residue.

Optionally print a header, and then a row for each hydrogen bond in the set using the iterprable version of the hbond show format formatted for easy parsing by R, Excel, etc.

References core::scoring::hbonds::HBond::acc_res(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), and core::scoring::hbonds::HBond::show().

void core::scoring::hbonds::NPDHBondSet::show ( pose::Pose const &  pose,
Size const  residue,
bool const  print_header = true 
) const
void core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom ( id::AtomID const &  jj_id)
private

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const NPDHBondSet hbond_set 
)
friend
bool operator== ( NPDHBondSet const &  a,
NPDHBondSet const &  b 
)
friend

equality operator

Member Data Documentation

id::AtomID_Map< utility::vector1< Real > > core::scoring::hbonds::NPDHBondSet::atom_hbond_energies_
private
id::AtomID_Map< utility::vector1< Real > > core::scoring::hbonds::NPDHBondSet::atom_hbond_sfxn_wtd_energies_
private

One score-function weighted energy per hbond per atom.

Referenced by derive_per_hbond_donor_and_acceptor_weights(), get_weights_for_one_partner_hbonder(), and get_weights_for_two_partner_hbonder().

id::AtomID_Map< utility::vector1< Real > > core::scoring::hbonds::NPDHBondSet::atom_hbond_weights_
private
utility::vector1< Real > core::scoring::hbonds::NPDHBondSet::dEtot_dEhb_
private
id::AtomID_Map< utility::vector1< utility::vector1< Real > > > core::scoring::hbonds::NPDHBondSet::dwt_dE_for_hbond_
private
EnergyMap core::scoring::hbonds::NPDHBondSet::sfxn_weights_
private

The weights (in particular, for the npd_hbond_* terms) that will be used to determine the donor and acceptor weights.

Referenced by get_weights_for_one_partner_hbonder(), and get_weights_for_two_partner_hbonder().


The documentation for this class was generated from the following files: